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PiElectronegativity.java
/*  $Revision: 10199 $ $Author: rajarshi $ $Date: 2008-02-21 19:19:31 +0100 (Thu, 21 Feb 2008) $
 *
 *  Copyright (C) 2008  Miguel Rojas <miguelrojasch@yahoo.es>
 *
 *  Contact: cdk-devel@list.sourceforge.net
 *
 *  This program is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public License
 *  as published by the Free Software Foundation; either version 2.1
 *  of the License, or (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public License
 *  along with this program; if not, write to the Free Software
 *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.openscience.cdk.charges;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;

/**
 * Calculation of the electronegativity of orbitals of a molecule 
 * by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).
 *
 * @author       Miguel Rojas Cherto
 * @cdk.created  2008-104-31
 * @cdk.module   charges
 * @cdk.keyword  electronegativity
 */
@TestClass("org.openscience.cdk.charges.PiElectronegativityTest")
00041 public class PiElectronegativity {
      
    private GasteigerMarsiliPartialCharges peoe = null;
    private GasteigerPEPEPartialCharges pepe = null;
    
      /**Number of maximum iterations*/
00047       private int maxI = 6;
    /**Number of maximum resonance structures*/
00049       private int maxRS = 50;
      
      private IMolecule molPi;
      private IAtomContainer acOldP;
      private double[][] gasteigerFactors;
      
    /**
     * Constructor for the PiElectronegativity object.
     */
00058     public PiElectronegativity() {
      this(6, 50);
    }

    /**
     * Constructor for the Electronegativity object.
     * 
     * @param maxIterations         The maximal number of Iteration  
     * @param maxResonStruc         The maximal number of Resonance Structures
     */
00068     public PiElectronegativity( int maxIterations, int maxResonStruc) {
      peoe = new GasteigerMarsiliPartialCharges();
      pepe = new GasteigerPEPEPartialCharges();
      maxI = maxIterations;
      maxRS = maxResonStruc;
    }

    /**
     * calculate the electronegativity of orbitals pi.
     *
     * @param ac                    IAtomContainer
     * @param atom                  atom for which effective atom electronegativity should be calculated     
     * 
     * @return piElectronegativity
     */
    @TestMethod("testCalculatePiElectronegativity_IAtomContainer_IAtom")
00084     public double calculatePiElectronegativity(IAtomContainer ac,
                                               IAtom atom){

      return calculatePiElectronegativity(ac, atom, maxI, maxRS);
      }
    /**
     * calculate the electronegativity of orbitals pi.
     *
     * @param ac                    IAtomContainer
     * @param atom                  atom for which effective atom electronegativity should be calculated     
     * @param maxIterations         The maximal number of Iteration  
     * @param maxResonStruc         The maximal number of Resonance Structures
     * 
     * @return piElectronegativity
     */
    @TestMethod("testCalculatePiElectronegativity_IAtomContainer_IAtom_Int_Int")
00100     public double calculatePiElectronegativity(IAtomContainer ac,
                                               IAtom atom,
                                               int maxIterations,
                                               int maxResonStruc) {
      maxI = maxIterations;
      maxRS = maxResonStruc;
      
      double electronegativity = 0;

        try {
            if(!ac.equals(acOldP)){
                  molPi = ac.getBuilder().newMolecule(ac);
                  
                peoe = new GasteigerMarsiliPartialCharges();
                  peoe.assignGasteigerMarsiliSigmaPartialCharges(molPi, true);
                        IAtomContainerSet iSet = ac.getBuilder().newAtomContainerSet();
                  iSet.addAtomContainer(molPi);
                  iSet.addAtomContainer(molPi);
      
                  gasteigerFactors = pepe.assignrPiMarsilliFactors(iSet);
                  
                  acOldP = ac;
            }           
            IAtom atomi = molPi.getAtom(ac.getAtomNumber(atom));
            int atomPosition = molPi.getAtomNumber(atomi);
            int stepSize = pepe.getStepSize();
            int start = (stepSize * (atomPosition) + atomPosition);
            double q = atomi.getCharge();
                if(molPi.getConnectedLonePairsCount(molPi.getAtom(atomPosition)) > 0 ||
                        molPi.getMaximumBondOrder(atomi) != IBond.Order.SINGLE ||
                                    atomi.getFormalCharge() != 0){
                  return ((gasteigerFactors[1][start]) + (q * gasteigerFactors[1][start + 1]) + (gasteigerFactors[1][start + 2] * (q * q)));
                }
            } catch (Exception e) {
                  e.printStackTrace();
            }

            return electronegativity;        
    }
    
    /**
     * set the maximal number of Iterations.
     * 
     * @param maxIterations The number maximal of iterations
     */
      @TestMethod("testSetMaxIterations_Int")
00146     public void setMaxIterations(int maxIterations){
      maxI = maxIterations;
    }

    /**
     * set the maximal number of resonance structures.
     * 
     * @param maxResonStruc The number maximal of resonance structures
     */
      @TestMethod("testSetMaxResonStruc_Int")
00156     public void setMaxResonStruc(int maxResonStruc){
      maxRS = maxResonStruc;
    }
    
    /**
     * get the maximal number of Iterations.
     * 
     * @return The number maximal of iterations
     */
      @TestMethod("testGetMaxIterations")
00166     public int getMaxIterations(){
      return maxI;
    }

    /**
     * get the maximal number of resonance structures.
     * 
     * @return The number maximal of resonance structures
     */
      @TestMethod("testGetMaxResonStruc")
00176     public int getMaxResonStruc(){
      return maxRS;
    }
    
    
}


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